Saturday, June 28, 2014

Twenty years ago yesterday, cognitive
scientist Stevan Harnad posted
a message on a mailing list, a
message he headed “A Subversive Proposal”. This called on all researchers
to make copies of the papers they published in scholarly journals freely
available on the Internet.

Today the Subversive Proposal is viewed
as one of the seminal texts of the open access movement.

To celebrate the 20th anniversary of the
Subversive Proposal, I emailed Harnad nine questions yesterday. These questions are published below, with Harnad’s answers attached.

Stevan Harnad

Q&A

RP:
Today is the 20th anniversary of the Subversive Proposal, a 496-word
online message you posted to a mailing list on June 27th
1994 in which you called on researchers to make copies of all the papers they published
in scholarly journals freely available on the Internet. The message sparked a
heated online debate that later formed the basis of a
book. What stimulated you to make that posting, and why do you think it
attracted as much attention and disagreement as it did?

(2)I also had a
strong belief in the creative power of interactive written dialogue, which became even stronger with the advent of the
online medium. (I had dubbed this “scholarly skywriting.”)

For scholarly skywriting to work, it has to be
accessible online. But although I knew about the price of subscriptions and the
serials crisis at the time, that was not my primary motivation: open online access and interaction was
(and still is). (I explained this more fully in your 2007 interview.)

As to attention: I’d have much been much happier if it
had attracted action rather than just attention! The disagreement (which is
always welcome, and can even be creative) was about
the things we will go on to discuss further below: Green vs. Gold OA and, to a
lesser extent, Gratis vs. Libre OA.

RP:
Looking back, what contribution would you say the Subversive Proposal has made to
the development of the OA movement, which in fact really only became a movement
7 years later (in 2001), when the term open access was adopted at the meeting where
the Budapest Open Access Initiative was planned and articulated?

SH: I’m not sure. What I tried to urge
all scholars to do in 1994 (self-archive their journal articles) some had
already been doing for years (notably computer scientists in anonymous FTP archives since the 1980’s and physicists in arXiv since 1991), but
I’m not aware that the self-archiving rate increased appreciably after my
proposal. The proposal may have created a bit of a flurry, but it was a
notional flurry: it was not heeded when it came to actual action
(self-archiving).

“BOAI
OA Strategy II” was OA journal publishing (“Gold OA”) and
that option (though it too was mentioned in the Subversive Proposal as the
likely end-game, after universal Green OA had prevailed) seems to have captured
people’s imaginations more than Green OA did. In fact, across the years since
1990 authors were providing little OA at all, though of the minority who were
providing OA, 2-3 times as many provided Green than Gold (and this is still true).

So,
again, I don’t see much practical
effect of the Subversive Proposal, either in 1994 or in the subsequent
half-decade. Nor did Green OA begin to come into its own when I commissioned
(and Rob Tansley created)
the first free software for creating Green OA institutional repositories in
2000. BOAI helped; but the first real sign of progress came with the outcome of
the 2004
UK Parliamentary Committee (which you phoned me in Barcelona to report,
Richard!). The committee recommended following the proposal — by me and others —
that UK research funders and universities should mandate (require) Green OA.
(The Committee only recommended some experimental support for Gold OA.) After
that, mandates
began to grow (though still very slowly).

Tuesday, June 17, 2014

On
May 15, 2014 both the Chinese Academy of Sciences (CAS) and
the National Natural Science Foundation of China (NSFC) announced new
open access policies.

Prof. Yonghe Zheng

Both funders’ policies require that all papers resulting from funded projects must be deposited in online repositories and made
publicly accessible within 12 months of publication — a model pioneered by the
US National Institutes of Health (NIH)
in 2008, when it introduced its influential Public Access Policy.

As
a result of the new Chinese policies there will be a significant increase in
the number of research papers freely available, not least because it comes at a
time when the number of papers published by Chinese researchers is growing
rapidly. In reporting
news of the policies, Nature indicated that
Chinese research output has grown from 48,000 articles in 2003, or 5.6% of the
global total, to more than 186,000 articles in 2012, or 13.9%.

Of
the latter figure, more than 100,000 papers, or 55.2% of Chinese output, involved some funding
from the NSFC. Below I publish a Q&A conducted by email with Prof. Yonghe Zheng, Deputy Director General of the Bureau of Policy, NSFC.

The
interview begins

Q:
NSFC recently announced an open access policy. As I understand it, this
policy will require researchers to deposit the final, peer-reviewed manuscripts
of research articles funded by NSFC into the organisation's repository and made
open access 12 months after publication. The policy also says that earlier open access should be provided where the publisher allows. Presumably researchers will be able to choose to
publish their papers either in subscription journals (and then self-archive
them as green OA) or in open access journals (gold OA)

A: Yes, the
researchers can choose to publish their papers in subscription journals or OA
journals as they like.

Q:
Does NSFC have a view on which form of OA is preferable and /or what percentage
of the papers that will be deposited under the policy will be gold and what
percentage green? And does it expect this percentage to change over time? Is
green OA seen as a transition arrangement before moving to a fully gold OA
environment for instance?

A: NSFC does not have
any policy presumption on the percentage of green OA and gold OA papers, and we
do not prefer researchers to publish papers in green or gold OA journals. The
percentage of green/gold OA papers is naturally produced right now, and we anticipate
this percentage will change over time. I guess gold OA is likely to take a much
more important role in a decade or so.

Q:
You say that the percentage of green and gold is naturally produced now.
Presumably this means that some researchers are already embracing OA. If so,
can you give me some estimate of the percentage of NSFC papers that are being
made OA today, and what percentage of that percentage is green OA and what
percentage is gold OA?

A: We know from
experience that many researchers we fund are paying APCs to publish OA articles
today, and many have deposited their AAM (author accepted manuscript) in the
institutional repository of their organisation, like the one at CAS. But at the
moment we do not have any statistics or reasonable estimates on the percentages
of NSFC papers made OA. We would certainly like to develop that capacity as we
implement our OA policy.

Q: Does NSFC allow researchers to use money from their grants to pay for gold OA? If so, are there any rules on how much they are able to spend on publishing a paper?

A: NSFC allows researchers
to use the funding to pay for gold OA papers as they did before to pay journals
to publish general papers under the funding plan.

Q:
Does NSFC have a separate gold OA fund that researchers can apply to in order
to pay for gold OA? If not, do you expect that such a fund will be set up in
the future?

A: We have no
specific fund for gold OA, but I am aware that other funding agencies in the
world have these kind of funds. We need to study how to promote OA development
in a sustainable way. Personally, I do not think it would be easy in NSFC to
set up this kind of fund. Certainly we would need to consider a number of questions
— fairness, for example, and the budgetary implications etc.

Q: Does NSFC have any bulk publishing/
membership agreements in place with scholarly publishers with regard to
publishing papers gold OA (e.g. similar to the one CAS signed with BMC in 2009)? If so,
can you give me the details? If not, does it expect to enter into similar
agreements in the future?

A: Right now, we
still have no agreement with regard to publishing OA papers with publishers. Some
publishers are very interested in cooperating with us to promote OA. We need to
do more evaluation before we design our policy plan.

Q:
I believe that the policy has immediate effect. However, I do not think that
the NSFC yet has a repository. What should researchers do in the meantime, and
when do you expect the NSFC repository to become available?

A: We need to develop
a repository in NSFC and I hope it will be ready before the end of 2016. Until
then researchers will need to provide deposit information in their project
reports, but they will not need to do any additional work before the repository
is ready.

Q:
You say that researchers need to provide deposit information in their project
reports. Can I just check: This means that researchers will not need to deposit
their papers until the repository is ready in 2016? If they do need to deposit
now, where can they deposit their papers today?

A: As I say, NSFC is
working to have its repository ready before the end of 2016 so that researchers
can deposit their funded papers. In the meantime, we encourage them to deposit
their papers in their respective institutional repositories. By the way, researchers
are asked to provide the basic information of their publications in their
annual report, and this information (including the abstracts of papers) is available
on the Information Sharing Serving Website of NSFC here.

Q:
Is NSFC building its repository itself, or will it outsource the work? If the
latter, who do you expect to build the NSFC repository?

A: The NSFC IT centre
will be in charge of calling for a bid for the development of the repository.

Monday, June 09, 2014

Today the world is awash with OA
advocates, and the number of them grows year by year. But it was not always
thus.

Subbiah Arunachalam

When Chennai-based information scientist Subbiah Arunachalam began calling for OA, for instance, there were hardly
any other OA advocates in India, and not a great many more in the rest of the world
either.

Yet like all developing countries, India
faced (and continues to face) a serious access problem with regard to the
scholarly literature — a function of the fact that the costs of subscribing to scholarly journals
are very high, and these costs consistently rise at a faster rate than overall
inflation. As a result, Indian scientists do not have access to all the
journals they need to do their job properly.

Arunachalam had long been puzzling over how
India’s access problem could be solved, and he had (unsuccessfully) tried a number
of ways to resolve it himself. Then in 1996 his attention was drawn to Stevan
Harnad’s 1994 Subversive Proposal — which called on all researchers to self-archive
their papers on the Internet so that they were free for anyone to read.

Immediately seeing the potential of
self-archiving, or what later became known as Green OA, Arunachalam
decided to organise a two-day workshop at the MS Swaminathan Research
Foundation (MSSRF)
Chennai, to which he invited Harnad. This was in 2000.

Since then Arunachalam has devoted a great deal of time and energy advocating for OA in India, an activity that must at
times have been a somewhat lonely experience. As the manager of Library and
Information Services at the International Crops Research Institute for Semi-Arid
Tropics (ICRISAT)
Muthu Madhan put it recently, “OA advocacy in India can be characterised as mostly
a one-man effort by Prof. Subbiah Arunachalam.”

What drives Arunachalam is a firm belief that open access holds out the promise of a faster and more effective system for creating and sharing new knowledge, one, moreover, that will not discriminate against the developing world in the way the current subscription system does. And this belief is rooted in a lifetime's experience as an editor of scientific journals, a student of science
(electrochemistry), and a period working as secretary of the Indian Academy
of Sciences.

Currently Arunachalam is a distinguished
fellow with the Centre for Internet & Society (CIS), and an Honorary Fellow of the UK’s CILIP. He also teaches science writing to
students of journalism.

(More on Arunachalam’s background and
career is available in three earlier interviews undertaken in 2006 and 2010 — here, here
and here).

Looking back, what does Arunachalam feel
has been achieved since he began his OA advocacy 14 years ago, and how would he
characterise the current state of OA in India? To find out, I put to him recently the ten
questions below.

Monday, June 02, 2014

Utopia Documents is a novel tool
for interacting with the scientific literature. Developed in 2009, it is a free
PDF reader that can connect the static content of scientific articles to the
dynamic world of online content.

This week Utopia will be released as an open source project. It will also become the platform for a new
crowdsourcing tool called Lazarus. With Lazarus, it is hoped to recover large
swathes of the legacy data currently imprisoned in the charts, tables, diagrams
and free-text of life science papers published in PDF files. This information
will then be made available as an open access database.

The developer of Utopia is computer
scientist Steve Pettifer, currently based at the University of Manchester. In a recent email
conversation Pettifer explained to me the background to Utopia, and what he
hopes to achieve with Lazarus.

Steve Pettifer

One
of the long-standing debates within the open access movement is whether
priority should be given to advocating for gratis OA (no cost
access to read research papers), or libre OA (no cost
access to read plus the right to reuse/repurpose
papers).

Advocates
for libre OA argue that since the
benefits it provides are much greater than gratis OA, libre OA should be
prioritised. Advocates for gratis OA respond that since
gratis OA is achievable much more quickly and easily (and without additional
cost to the research community), it should
be prioritised. Besides, they add, very few researchers want to reuse research
papers in any case.

In
reply to this last point, libre OA advocates retort that the issue is not just
one of reuse, but having the ability to text and data mine papers in order to create
new services and databases and generate new knowledge. For this reason, they
say, it is vital that papers are licensed under permissive Creative Commons
licences that allow reuse (i.e. libre OA).

Passive reading

For
similar reasons libre OA advocates dislike the widespread use of PDFs today.
Designed to ensure that the (print-focused) layout of a document is the same
whatever system it is displayed in, the Adobe Acrobat format is not conducive
to text mining. So while it is fine for human readers, computers struggle to
make sense of a PDF.

It
may, for instance, not include information about who authored the document or
the nature of the content in a form that machines can understand, since this
would require the inclusion of metadata. While metadata can be inserted into PDF
files, publishers/authors rarely go to the effort of inserting it. For this
reason PDFs generally also do not have an explicit machine readable
licence embedded in them to signal what can legally be done with the content.

In
addition, any diagrams and charts in a PDF file will be static images, so
machines cannot extract the underlying data in order to reuse or process the
information.

Critics
of the PDF also dislike the fact that it permits only passive reading. This
means that scientists are not fully able to exploit the dynamic and linked
nature of the Web. In fact, researchers often simply print PDF files out and
read them offline. For these reasons, libre OA
advocates,
computer scientists, and forward-looking publishers (particularly OA
publishers) are constantly trying to wean researchers off PDFs in favour of
reading papers online in HTML.

Over
a decade ago, for instance, the Biochemical
Journal spent a great deal of time and effort revamping its site. It did
this sufficiently well that it won the 2007 ALPSP/Charlesworth
Award for Best Online Journal — on the grounds that it had successfully
“overcome the limitations of print and exploited the flexibility of the digital
environment”.

But
to the frustration of the journal’s publisher — Portland Press — despite all
its efforts scientists simply carried on downloading the papers as PDF files.

Researchers,
it turns out, still much prefer PDFs.

The
question is however: Do PDF files allow scientists to make best us of the Web? This
thought occurred to Steve Pettifer in 2008, as he watched a room full of life
scientists trying to combine the work of two separate labs by downloading PDFs,
printing them off, and then rapidly scanning the information in them. Surely, he
thought, this is not a very efficient way of doing science in the 21st
Century?

Since
Portland Press had reached the same conclusion it offered to fund Pettifer and
his colleague Terri Attwood to come up
with a solution that would combine the appeal, portability, and convenience of
the PDF with the dynamic qualities of the Web.